BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0022.0289.p (655 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulat... 1241 0.0 gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein... 252 7e-68 gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcriptio... 249 7e-67 gi|300313916|ref|YP_003778008.1| two component response regulato... 237 2e-63 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 232 7e-62 >gi|300313867|ref|YP_003777959.1| phenol-degradative gene regulator transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 611 Score = 1241 bits (3212), Expect = 0.0, Method: Compositional matrix adjust. Identities = 611/611 (100%), Positives = 611/611 (100%) Query: 45 MPSSPRISLAEMARHQGGGLSSAGTDRWSVDAHPTLADLSECLFFSPGDGRIWLNDQRML 104 MPSSPRISLAEMARHQGGGLSSAGTDRWSVDAHPTLADLSECLFFSPGDGRIWLNDQRML Sbjct: 1 MPSSPRISLAEMARHQGGGLSSAGTDRWSVDAHPTLADLSECLFFSPGDGRIWLNDQRML 60 Query: 105 LIHSRSMGTLRRELIDQLGIDQARGLLTRAGYISGARDAQLVRERWPDADPSTILMAGTR 164 LIHSRSMGTLRRELIDQLGIDQARGLLTRAGYISGARDAQLVRERWPDADPSTILMAGTR Sbjct: 61 LIHSRSMGTLRRELIDQLGIDQARGLLTRAGYISGARDAQLVRERWPDADPSTILMAGTR 120 Query: 165 LHTLEGLVKVVPVSFSYDPETGRYEGEFLWHNSCEADEHLAAYGVATAPSCWQQVGYAIG 224 LHTLEGLVKVVPVSFSYDPETGRYEGEFLWHNSCEADEHLAAYGVATAPSCWQQVGYAIG Sbjct: 121 LHTLEGLVKVVPVSFSYDPETGRYEGEFLWHNSCEADEHLAAYGVATAPSCWQQVGYAIG 180 Query: 225 YVSTLLGHLVIFREVQCRAMGTAHCRVIGRSAELWSDAEEDLRYLNAQDFVGSGMLASEA 284 YVSTLLGHLVIFREVQCRAMGTAHCRVIGRSAELWSDAEEDLRYLNAQDFVGSGMLASEA Sbjct: 181 YVSTLLGHLVIFREVQCRAMGTAHCRVIGRSAELWSDAEEDLRYLNAQDFVGSGMLASEA 240 Query: 285 DASAEDGAQGAGEQDDDTDLVTALVGTSSAFNAACHLLNRVAATDATVLFTGESGVGKER 344 DASAEDGAQGAGEQDDDTDLVTALVGTSSAFNAACHLLNRVAATDATVLFTGESGVGKER Sbjct: 241 DASAEDGAQGAGEQDDDTDLVTALVGTSSAFNAACHLLNRVAATDATVLFTGESGVGKER 300 Query: 345 FARMLHQIGKRAKRACIAINCAAIPETLIEAELFGVERGAYTGATQSRAGRFELADGGTL 404 FARMLHQIGKRAKRACIAINCAAIPETLIEAELFGVERGAYTGATQSRAGRFELADGGTL Sbjct: 301 FARMLHQIGKRAKRACIAINCAAIPETLIEAELFGVERGAYTGATQSRAGRFELADGGTL 360 Query: 405 FLDEVGTLSLVAQGKLLRVLQEGEFERVGSARPVKVDVRVVAATNEDLAQAVREGRFRQD 464 FLDEVGTLSLVAQGKLLRVLQEGEFERVGSARPVKVDVRVVAATNEDLAQAVREGRFRQD Sbjct: 361 FLDEVGTLSLVAQGKLLRVLQEGEFERVGSARPVKVDVRVVAATNEDLAQAVREGRFRQD 420 Query: 465 LFFRLNVFPIHLPPLRERRDDIPLLMNHFLKLYGQRHGIAVRGFTQRAIQALLNYSFPGN 524 LFFRLNVFPIHLPPLRERRDDIPLLMNHFLKLYGQRHGIAVRGFTQRAIQALLNYSFPGN Sbjct: 421 LFFRLNVFPIHLPPLRERRDDIPLLMNHFLKLYGQRHGIAVRGFTQRAIQALLNYSFPGN 480 Query: 525 IRELQNLIERGVILAQGHPLDLPHMFISGERLNDEVLSLALQGETGMLAGKSVEKSVEKS 584 IRELQNLIERGVILAQGHPLDLPHMFISGERLNDEVLSLALQGETGMLAGKSVEKSVEKS Sbjct: 481 IRELQNLIERGVILAQGHPLDLPHMFISGERLNDEVLSLALQGETGMLAGKSVEKSVEKS 540 Query: 585 VAHPTAQGLLDVLRQWRQEAAGEAAALTLPEMERRLIAEAIERAEGNLSAAARLLGISRA 644 VAHPTAQGLLDVLRQWRQEAAGEAAALTLPEMERRLIAEAIERAEGNLSAAARLLGISRA Sbjct: 541 VAHPTAQGLLDVLRQWRQEAAGEAAALTLPEMERRLIAEAIERAEGNLSAAARLLGISRA 600 Query: 645 QLAYRQQKGQG 655 QLAYRQQKGQG Sbjct: 601 QLAYRQQKGQG 611 >gi|300312179|ref|YP_003776271.1| nif-specific regulatory protein [Herbaspirillum seropedicae SmR1] Length = 542 Score = 252 bits (643), Expect = 7e-68, Method: Compositional matrix adjust. Identities = 162/444 (36%), Positives = 237/444 (53%), Gaps = 44/444 (9%) Query: 219 VGYAIGYVSTLLGHLVIFREVQCRAMGTAH--------CRVIGRSAELWSDAEEDLRYLN 270 VG I +LG L +FR+ Q + H +IG++ L+ + + L Sbjct: 125 VGVPIKAAREMLGVLCVFRDGQSPSRSVDHEVRLLTMVANLIGQTVRLYRSVAAERQQLQ 184 Query: 271 AQDFVGSGMLASEADASAEDGAQGAGEQDDDTDLVTALVGTSSAFNAACHLLNRVAATDA 330 + S L QG + D+ ++G S A +++ A + + Sbjct: 185 EEKRQLSRQL------------QGKYKLDN-------VIGISKAMQEVFAQVHQSAPSRS 225 Query: 331 TVLFTGESGVGKERFARMLHQIGKRAKRACIAINCAAIPETLIEAELFGVERGAYTGATQ 390 T+L GESG GKE AR +H + R I +NCAA+ ETL+E+ELFG E+GA+TGA Sbjct: 226 TMLLRGESGTGKEVIARAIHYLSPRKDGPFIKVNCAALSETLLESELFGHEKGAFTGAQG 285 Query: 391 SRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEGEFERVGSARPVKVDVRVVAATNE 450 R GRFELA GGTLFLDE+G +S Q KLLRVLQE EFERVG +R +KVDVR+V ATN Sbjct: 286 ERKGRFELAHGGTLFLDEIGEISPAFQAKLLRVLQEREFERVGGSRSIKVDVRLVTATNR 345 Query: 451 DLAQAVREGRFRQDLFFRLNVFPIHLPPLRERRDDIPLLMNHFLKLYGQRHGIAVRGFTQ 510 DL +AV +G FR DL++R+NV I +PPLRERR+DIP L+ HFL+ + + A+ + Sbjct: 346 DLEKAVAKGEFRADLYYRINVVSIFIPPLRERREDIPYLVEHFLEKFRVENQRAMVAMSP 405 Query: 511 RAIQALLNYSFPGNIRELQNLIERGVILAQGHPLDLPHMFISGERLNDEVLSLALQGETG 570 +A++ ++N +PGN+REL+N +ER + +G + H + +VL Q + Sbjct: 406 QAMKVMMNCYWPGNVRELENCVERTATMMRGDLITEVHFSCQQNKCLTKVLHEPGQQQPV 465 Query: 571 MLAGKSVEKSVEKSVAH--PTAQGLLDVLRQWRQEAAGEAAALTLPEMERRLIAEAIERA 628 ++ +E+ AH P++ + A + A P ER + A+E+ Sbjct: 466 VVV------PLERISAHTAPSSPSGM---------AKDKPLAAAPPTSERERLIWAMEQC 510 Query: 629 EGNLSAAARLLGISRAQLAYRQQK 652 + AAR L IS Q+ Y QK Sbjct: 511 GWVQAKAARALNISPRQMGYALQK 534 >gi|300311822|ref|YP_003775914.1| sigma-54 dependent transcription regulator [Herbaspirillum seropedicae SmR1] Length = 526 Score = 249 bits (635), Expect = 7e-67, Method: Compositional matrix adjust. Identities = 150/344 (43%), Positives = 204/344 (59%), Gaps = 32/344 (9%) Query: 308 LVGTSSAFNAACHLLNRVAATDATVLFTGESGVGKERFARMLHQIGKRAKRACIAINCAA 367 L+G S A + A +D TVL GE+G GKE A LH RA + I++NCAA Sbjct: 200 LIGQSPAHRQLMQEIGMAAPSDMTVLVAGETGTGKELVAHALHAASPRAHKPMISLNCAA 259 Query: 368 IPETLIEAELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEG 427 +P+TL+E+ELFG RGA++GA R G+FE+ADGGTLFLDEVG L L Q KLLRVLQ G Sbjct: 260 LPDTLVESELFGHVRGAFSGAVADRRGKFEMADGGTLFLDEVGELPLAVQAKLLRVLQSG 319 Query: 428 EFERVGSARPVKVDVRVVAATNEDLAQAVREGRFRQDLFFRLNVFPIHLPPLRERRDDIP 487 + +RVGS R +VDVR++AATN DLA V+ G FR D + RL+VFPI +PPLRER D+ Sbjct: 320 QLQRVGSDREHRVDVRLIAATNRDLADEVKRGHFRADFYHRLSVFPIRVPPLRERGRDVL 379 Query: 488 LLMNHFLKLYGQRHGIAVRGFTQRAIQALLNYSFPGNIRELQNLIERGVILAQGHPLDLP 547 LL +FL+ R G++ + A +ALL+Y++PGNIREL++LI R + + Sbjct: 380 LLAGYFLEQNRARLGLSSLRLSADAQRALLDYAWPGNIRELEHLIGRSALRS-------- 431 Query: 548 HMFISGERLNDEVLSL---ALQGETGMLAG-KSVEKSVEKSVAHPTAQG-LLDVLRQWRQ 602 ++ R +L+L AL+ LA + E S+ A G L D L ++ Sbjct: 432 ---LATHRTRPTILTLDAAALELPAPSLATVAAAEPSLPAESTPAQASGSLRDALERY-- 486 Query: 603 EAAGEAAALTLPEMERRLIAEAIERAEGNLSAAARLLGISRAQL 646 ER+L++ A++R GNL+A AR LG+ RA L Sbjct: 487 --------------ERQLVSAALQRHGGNLAATARELGVDRANL 516 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 237 bits (605), Expect = 2e-63, Method: Compositional matrix adjust. Identities = 149/348 (42%), Positives = 199/348 (57%), Gaps = 39/348 (11%) Query: 308 LVGTSSAFNAACHLLNRVAATDATVLFTGESGVGKERFARMLHQIGKRAKRACIAINCAA 367 LVG S A + R A +DATVL GE+G GKE AR LH+ G RA R +A+NCAA Sbjct: 136 LVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVNCAA 195 Query: 368 IPETLIEAELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEG 427 IP LIE+ELFG +GA++GAT R GRF+ ADGGTLFLDE+G + L Q K+LRVLQE Sbjct: 196 IPAELIESELFGHVKGAFSGATSPRLGRFQEADGGTLFLDEIGDMELATQAKILRVLQER 255 Query: 428 EFERVGSARPVKVDVRVVAATNEDLAQAVREGRFRQDLFFRLNVFPIHLPPLRERRDDIP 487 E VG + V+VDVRV+AAT+ DL + +GRFR+DL++RL V I +P LRER DI Sbjct: 256 ELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPGDIL 315 Query: 488 LLMNHFLKLYGQRHGIAVRGFTQRAIQALLNYSFPGNIRELQNLIERGVILAQGHPLDLP 547 + HFL+ G G A + + A + LL +++PGN+REL+N +ER +++ G Sbjct: 316 TIAEHFLRQLG---GDAPKRISPAAARLLLQHAWPGNVRELRNTMERAAVMSHG------ 366 Query: 548 HMFISGERLNDEVLSLALQGETGMLAGKSVEKSVEKSVAHPTAQGLLDVLRQWRQEAAGE 607 + I E + G+ A + S G L Sbjct: 367 -LCIEAE-------------DIGLSARPPAGAASAASAPAIDWDGPL------------- 399 Query: 608 AAALTLPEMERRLIAEAIERAEGNLSAAARLLGISRAQLAYRQQKGQG 655 A+ L E+ER +I A++ A GN + AAR LGISR QL YR+ + G Sbjct: 400 --AVALAEVERVMIERALQGAAGNRAEAARRLGISRQQL-YRRLEEAG 444 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 232 bits (592), Expect = 7e-62, Method: Compositional matrix adjust. Identities = 135/339 (39%), Positives = 189/339 (55%), Gaps = 46/339 (13%) Query: 308 LVGTSSAFNAACHLLNRVAATDATVLFTGESGVGKERFARMLHQIGKRAKRACIAINCAA 367 L+ + A C + +VA + A+V+ G SG GKE AR LHQ+ R+ R +AINCAA Sbjct: 148 LITRDAGMLAVCRSIEKVAPSSASVMLLGSSGTGKEVLARALHQLSPRSGRRFMAINCAA 207 Query: 368 IPETLIEAELFGVERGAYTGATQSRAGRFELADGGTLFLDEVGTLSLVAQGKLLRVLQEG 427 IPE L+E+ELFG E+GA+TGA + G+ ELA GGT FLDEVG L + Q KLLR LQE Sbjct: 208 IPENLLESELFGYEKGAFTGAAKQTIGKVELAHGGTFFLDEVGDLPMPLQAKLLRFLQER 267 Query: 428 EFERVGSARPVKVDVRVVAATNEDLAQAVREGRFRQDLFFRLNVFPIHLPPLRERRDDIP 487 ERVG + VDVRV+ AT+++L + G FR+DL++RL I +P L+ER D Sbjct: 268 VIERVGGHTEIPVDVRVICATHQNLKELTASGGFREDLYYRLCEIIIKIPALKERHGDAV 327 Query: 488 LLMNHFLKLYGQRHGIAVRGFTQRAIQALLNYSFPGNIRELQNLIERGVILAQGHPLDLP 547 LL HF++ + + G A +Q A+ A+ Y +PGN+RE++N + R VI+A Sbjct: 328 LLARHFVQKFCAKEGRATLHLSQDAVAAIERYEWPGNVREMENCVMRAVIMA-------- 379 Query: 548 HMFISGERLNDEVLSLALQGETGMLAGKSVEKSVEKSVAHPTAQGLLDVLRQWRQEAAGE 607 G+++ E L L+++G A P LRQ R EA Sbjct: 380 ----DGQQITAEDLGLSVEGRE----------------AEPLN------LRQVRDEA--- 410 Query: 608 AAALTLPEMERRLIAEAIERAEGNLSAAARLLGISRAQL 646 ER+ + +A+ R +GN+ AA LLG+SR L Sbjct: 411 ---------ERKAVVKALTRMDGNILKAAELLGVSRPTL 440 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.321 0.136 0.398 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 2,048,802 Number of extensions: 89489 Number of successful extensions: 318 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 304 Number of HSP's successfully gapped: 12 Length of query: 655 Length of database: 1,619,870 Length adjustment: 91 Effective length of query: 564 Effective length of database: 1,188,985 Effective search space: 670587540 Effective search space used: 670587540 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 134 (56.2 bits)